BioC 3.5: CHECK report for AllelicImbalance on malbec2

Package: AllelicImbalance

Version: 1.14.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz

StartedAt: 2017-10-17 21:06:30 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:13:04 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 393.6 seconds

RetCode: 0

Status: OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AllelicImbalance’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 17.264  4.656  25.436
import-bam           15.044  0.096  15.151
annotation-wrappers   5.652  0.048   6.022
getAlleleCounts       5.536  0.012   5.553
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AllelicImbalance)

name	user	system	elapsed
ASEset-barplot	0.328	0.012	0.341
ASEset-class	0.584	0.000	0.583
ASEset-filters	0.076	0.000	0.077
ASEset-gbarplot	0.032	0.000	0.034
ASEset-glocationplot	4.572	0.036	4.612
ASEset-gviztrack	0.624	0.004	0.629
ASEset-scanForHeterozygotes	1.860	0.000	1.861
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.004	0.000	0.002
DetectedAI-class	0.044	0.000	0.046
DetectedAI-plot	1.660	0.000	1.747
DetectedAI-summary	0.06	0.00	0.06
GRvariants	0.000	0.004	0.002
GlobalAnalysis-class	0.000	0.000	0.002
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	1.276	0.000	1.278
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	5.652	0.048	6.022
annotationBarplot	0	0	0
barplot-lattice-support	0.172	0.000	0.173
binom.test	0.04	0.00	0.04
chisq.test	0.116	0.000	0.118
cigar-utilities	0.016	0.000	0.015
countAllelesFromBam	0.004	0.000	0.004
coverageMatrixListFromGAL	0.764	0.000	0.765
decorateWithExons	0.004	0.000	0.001
decorateWithGenes	0.000	0.000	0.002
defaultMapBias	0.032	0.000	0.034
defaultPhase	0.004	0.000	0.001
detectAI	0.060	0.000	0.059
fractionPlotDf	0.024	0.000	0.023
gba	0	0	0
genomatrix	0	0	0
genotype2phase	0.024	0.000	0.024
getAlleleCounts	5.536	0.012	5.553
getAlleleQuality	4.192	0.016	4.210
getAreaFromGeneNames	0.364	0.004	0.368
getDefaultMapBiasExpMean	0.02	0.00	0.02
getSnpIdFromLocation	17.264	4.656	25.436
histplot	0.000	0.000	0.001
implodeList-old	0.004	0.000	0.005
import-bam-2	0.004	0.000	0.006
import-bam	15.044	0.096	15.151
import-bcf	0.724	0.004	0.727
inferAlleles	0.068	0.000	0.067
inferAltAllele	0.012	0.000	0.012
inferGenotypes	0.060	0.004	0.062
initialize-ASEset	0.152	0.000	0.154
initialize-DetectedAI	0.040	0.000	0.039
initialize-GlobalAnalysis	0.004	0.000	0.004
initialize-RiskVariant	0.000	0.000	0.002
legendBarplot	0	0	0
locationplot	1.300	0.000	1.301
lva	3.500	0.000	3.498
lva.internal	0.188	0.000	0.188
makeMaskedFasta	0.736	0.000	0.736
mapBiasRef	0.008	0.000	0.009
minCountFilt	0.024	0.000	0.026
minFreqFilt	0.024	0.000	0.025
multiAllelicFilt	0.008	0.000	0.009
phase2genotype	0.016	0.000	0.015
phaseArray2phaseMatrix	0.008	0.000	0.006
phaseMatrix2Array	0.008	0.000	0.006
randomRef	0.012	0.000	0.010
reads	0	0	0
refAllele	0.012	0.000	0.012
regionSummary	0.316	0.000	0.314
scanForHeterozygotes-old	3.540	0.000	3.543

BioC 3.5: CHECK report for AllelicImbalance on malbec2

Summary

Command output